Starting phenix.real_space_refine on Sat Mar 16 14:01:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsm_36623/03_2024/8jsm_36623.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 76 5.16 5 C 9442 2.51 5 N 2512 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14856 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10897 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1289} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2015 Chain: "C" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 737 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 511 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 509 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9157 SG CYS A1150 50.021 51.096 98.488 1.00 96.82 S ATOM 9179 SG CYS A1153 52.834 48.431 97.974 1.00 94.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 266 " occ=0.44 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.56 Time building chain proxies: 9.42, per 1000 atoms: 0.63 Number of scatterers: 14856 At special positions: 0 Unit cell: (175.96, 138.61, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 76 16.00 P 10 15.00 O 2815 8.00 N 2512 7.00 C 9442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " Number of angles added : 2 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 58.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.672A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.134A pdb=" N CYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.725A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 99 through 122 removed outlier: 4.124A pdb=" N ILE A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.658A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.660A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 261 removed outlier: 3.597A pdb=" N ILE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.573A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.304A pdb=" N TYR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.508A pdb=" N HIS A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.745A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.038A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 515 through 521 removed outlier: 3.576A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.794A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.670A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.590A pdb=" N TYR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.733A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.268A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.939A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.611A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.922A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 948 through 955 removed outlier: 4.389A pdb=" N LYS A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.830A pdb=" N SER A 977 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 978' Processing helix chain 'A' and resid 980 through 994 removed outlier: 3.609A pdb=" N LEU A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 3.511A pdb=" N LEU A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.832A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.582A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.536A pdb=" N ASN A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.544A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.941A pdb=" N ALA A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.567A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.922A pdb=" N MET A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1273 removed outlier: 3.957A pdb=" N ARG A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.661A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 82 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 4.625A pdb=" N ASP B 123 " --> pdb=" O PRO B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 149 Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.703A pdb=" N ALA B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.723A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.940A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.667A pdb=" N ASP B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 119 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.891A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.673A pdb=" N ALA C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 removed outlier: 3.682A pdb=" N THR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.820A pdb=" N TYR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 117 Processing helix chain 'E' and resid 118 through 144 removed outlier: 4.185A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 3.701A pdb=" N LEU A 71 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 231 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.962A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 3.992A pdb=" N SER A1175 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.950A pdb=" N LYS B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3610 1.33 - 1.45: 2981 1.45 - 1.57: 8488 1.57 - 1.69: 19 1.69 - 1.81: 111 Bond restraints: 15209 Sorted by residual: bond pdb=" CA ASN A 959 " pdb=" CB ASN A 959 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.51e-02 4.39e+03 4.77e+00 bond pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.37e-02 5.33e+03 3.54e+00 bond pdb=" N SER C 179 " pdb=" CA SER C 179 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.34e+00 bond pdb=" CA ASP A 757 " pdb=" CB ASP A 757 " ideal model delta sigma weight residual 1.518 1.546 -0.028 2.08e-02 2.31e+03 1.86e+00 bond pdb=" C GLU C 178 " pdb=" O GLU C 178 " ideal model delta sigma weight residual 1.232 1.249 -0.017 1.32e-02 5.74e+03 1.71e+00 ... (remaining 15204 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.23: 493 106.23 - 113.16: 8281 113.16 - 120.10: 5291 120.10 - 127.03: 6452 127.03 - 133.97: 202 Bond angle restraints: 20719 Sorted by residual: angle pdb=" N GLN B 99 " pdb=" CA GLN B 99 " pdb=" CB GLN B 99 " ideal model delta sigma weight residual 110.40 116.55 -6.15 1.63e+00 3.76e-01 1.42e+01 angle pdb=" N GLU B 115 " pdb=" CA GLU B 115 " pdb=" CB GLU B 115 " ideal model delta sigma weight residual 110.28 116.06 -5.78 1.55e+00 4.16e-01 1.39e+01 angle pdb=" C GLN B 98 " pdb=" N GLN B 99 " pdb=" CA GLN B 99 " ideal model delta sigma weight residual 121.14 114.62 6.52 1.75e+00 3.27e-01 1.39e+01 angle pdb=" C LEU B 114 " pdb=" N GLU B 115 " pdb=" CA GLU B 115 " ideal model delta sigma weight residual 120.31 115.00 5.31 1.52e+00 4.33e-01 1.22e+01 angle pdb=" C SER A 750 " pdb=" N VAL A 751 " pdb=" CA VAL A 751 " ideal model delta sigma weight residual 121.97 128.08 -6.11 1.80e+00 3.09e-01 1.15e+01 ... (remaining 20714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 8986 35.69 - 71.39: 200 71.39 - 107.08: 15 107.08 - 142.77: 0 142.77 - 178.47: 1 Dihedral angle restraints: 9202 sinusoidal: 3739 harmonic: 5463 Sorted by residual: dihedral pdb=" O4' C G 7 " pdb=" C1' C G 7 " pdb=" N1 C G 7 " pdb=" C2 C G 7 " ideal model delta sinusoidal sigma weight residual -128.00 50.47 -178.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER A 431 " pdb=" C SER A 431 " pdb=" N ASP A 432 " pdb=" CA ASP A 432 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN E 99 " pdb=" C GLN E 99 " pdb=" N GLN E 100 " pdb=" CA GLN E 100 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1501 0.030 - 0.059: 599 0.059 - 0.089: 179 0.089 - 0.119: 89 0.119 - 0.148: 15 Chirality restraints: 2383 Sorted by residual: chirality pdb=" CA GLN B 99 " pdb=" N GLN B 99 " pdb=" C GLN B 99 " pdb=" CB GLN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA GLN E 99 " pdb=" N GLN E 99 " pdb=" C GLN E 99 " pdb=" CB GLN E 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ASP A1368 " pdb=" N ASP A1368 " pdb=" C ASP A1368 " pdb=" CB ASP A1368 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2380 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 892 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 893 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 893 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 893 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 959 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ASN A 959 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN A 959 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS A 960 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 314 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 315 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.022 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 119 2.62 - 3.19: 13003 3.19 - 3.76: 21730 3.76 - 4.33: 29295 4.33 - 4.90: 50655 Nonbonded interactions: 114802 Sorted by model distance: nonbonded pdb=" NE2 GLN E 99 " pdb=" OE1 GLN E 100 " model vdw 2.050 2.520 nonbonded pdb=" O ASN A 959 " pdb=" ND2 ASN A 959 " model vdw 2.206 2.520 nonbonded pdb=" O TYR A 32 " pdb=" OG1 THR A 70 " model vdw 2.223 2.440 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.270 2.520 nonbonded pdb=" OE1 GLU A1218 " pdb=" NH2 ARG A1247 " model vdw 2.271 2.520 ... (remaining 114797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 82 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 118 or (resid 119 and (name N or n \ ame CA or name C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 132 or (resid 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.000 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15209 Z= 0.174 Angle : 0.545 7.145 20719 Z= 0.289 Chirality : 0.038 0.148 2383 Planarity : 0.004 0.055 2616 Dihedral : 15.378 178.467 5656 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.71 % Favored : 93.97 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1843 helix: 1.94 (0.17), residues: 965 sheet: 1.32 (0.56), residues: 81 loop : -1.26 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1085 HIS 0.006 0.001 HIS B 166 PHE 0.014 0.001 PHE A 411 TYR 0.013 0.001 TYR A 800 ARG 0.007 0.000 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.633 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.2731 time to fit residues: 94.8025 Evaluate side-chains 202 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 chunk 144 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 663 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN A1333 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15209 Z= 0.218 Angle : 0.550 7.809 20719 Z= 0.282 Chirality : 0.040 0.146 2383 Planarity : 0.004 0.037 2616 Dihedral : 9.051 179.885 2164 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.41 % Favored : 93.26 % Rotamer: Outliers : 1.35 % Allowed : 7.69 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1843 helix: 2.10 (0.17), residues: 987 sheet: 1.21 (0.56), residues: 83 loop : -1.30 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.007 0.001 HIS B 166 PHE 0.016 0.001 PHE A 411 TYR 0.014 0.001 TYR B 142 ARG 0.006 0.000 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1112 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 230 ASP cc_start: 0.7877 (m-30) cc_final: 0.6696 (m-30) outliers start: 22 outliers final: 15 residues processed: 218 average time/residue: 0.2854 time to fit residues: 90.9083 Evaluate side-chains 215 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15209 Z= 0.330 Angle : 0.585 6.538 20719 Z= 0.303 Chirality : 0.041 0.141 2383 Planarity : 0.004 0.042 2616 Dihedral : 9.180 176.979 2164 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.63 % Favored : 93.04 % Rotamer: Outliers : 1.42 % Allowed : 10.09 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1843 helix: 1.98 (0.17), residues: 989 sheet: 1.10 (0.57), residues: 83 loop : -1.43 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS B 166 PHE 0.020 0.002 PHE A 411 TYR 0.014 0.002 TYR A 701 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 TYR cc_start: 0.8678 (m-10) cc_final: 0.8411 (m-10) REVERT: B 304 PRO cc_start: 0.7232 (Cg_exo) cc_final: 0.7010 (Cg_endo) outliers start: 23 outliers final: 19 residues processed: 219 average time/residue: 0.2744 time to fit residues: 87.7675 Evaluate side-chains 213 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.0470 chunk 159 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN A1111 GLN B 194 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15209 Z= 0.282 Angle : 0.557 6.774 20719 Z= 0.288 Chirality : 0.041 0.142 2383 Planarity : 0.004 0.041 2616 Dihedral : 9.267 176.697 2164 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.20 % Favored : 93.48 % Rotamer: Outliers : 2.58 % Allowed : 11.02 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1843 helix: 1.91 (0.17), residues: 997 sheet: 1.13 (0.58), residues: 83 loop : -1.46 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 191 HIS 0.006 0.001 HIS B 166 PHE 0.018 0.002 PHE A 411 TYR 0.013 0.002 TYR B 142 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1379 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4618 (tt) REVERT: A 1382 ASP cc_start: 0.7776 (t0) cc_final: 0.7368 (t0) REVERT: B 107 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 304 PRO cc_start: 0.7355 (Cg_exo) cc_final: 0.7113 (Cg_endo) outliers start: 42 outliers final: 29 residues processed: 224 average time/residue: 0.2763 time to fit residues: 90.2949 Evaluate side-chains 226 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15209 Z= 0.194 Angle : 0.538 11.818 20719 Z= 0.276 Chirality : 0.039 0.163 2383 Planarity : 0.004 0.038 2616 Dihedral : 9.223 178.152 2164 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.36 % Favored : 93.32 % Rotamer: Outliers : 1.91 % Allowed : 12.62 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1843 helix: 2.06 (0.17), residues: 990 sheet: 1.18 (0.58), residues: 83 loop : -1.44 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1019 HIS 0.006 0.001 HIS B 166 PHE 0.015 0.001 PHE A 411 TYR 0.012 0.001 TYR A 153 ARG 0.003 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1044 LEU cc_start: 0.8826 (tt) cc_final: 0.8451 (mp) REVERT: A 1379 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4691 (tt) REVERT: A 1382 ASP cc_start: 0.7739 (t0) cc_final: 0.7341 (t0) REVERT: B 107 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8663 (pp) REVERT: B 304 PRO cc_start: 0.7365 (Cg_exo) cc_final: 0.7143 (Cg_endo) outliers start: 31 outliers final: 24 residues processed: 219 average time/residue: 0.3000 time to fit residues: 97.7013 Evaluate side-chains 218 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15209 Z= 0.253 Angle : 0.551 9.734 20719 Z= 0.284 Chirality : 0.040 0.159 2383 Planarity : 0.004 0.039 2616 Dihedral : 9.238 177.147 2164 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.52 % Favored : 93.15 % Rotamer: Outliers : 2.52 % Allowed : 12.68 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1843 helix: 2.01 (0.17), residues: 991 sheet: 1.21 (0.58), residues: 83 loop : -1.47 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.007 0.001 HIS B 166 PHE 0.017 0.002 PHE A 411 TYR 0.013 0.001 TYR A 153 ARG 0.004 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 1044 LEU cc_start: 0.8835 (tt) cc_final: 0.8487 (mp) REVERT: A 1379 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4681 (tt) REVERT: A 1382 ASP cc_start: 0.7746 (t0) cc_final: 0.7358 (t0) REVERT: B 107 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8679 (pp) outliers start: 41 outliers final: 32 residues processed: 229 average time/residue: 0.2784 time to fit residues: 93.6502 Evaluate side-chains 234 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1094 ASN Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 0.0170 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15209 Z= 0.261 Angle : 0.557 8.691 20719 Z= 0.287 Chirality : 0.040 0.159 2383 Planarity : 0.004 0.039 2616 Dihedral : 9.239 176.839 2164 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.14 % Favored : 93.53 % Rotamer: Outliers : 2.34 % Allowed : 13.11 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1843 helix: 2.00 (0.17), residues: 992 sheet: 1.19 (0.58), residues: 83 loop : -1.48 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.006 0.001 HIS B 166 PHE 0.017 0.001 PHE A 411 TYR 0.014 0.001 TYR A 153 ARG 0.003 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 800 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7319 (p90) REVERT: A 1044 LEU cc_start: 0.8840 (tt) cc_final: 0.8497 (mp) REVERT: A 1379 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4738 (tt) REVERT: A 1382 ASP cc_start: 0.7764 (t0) cc_final: 0.7376 (t0) REVERT: B 107 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8681 (pp) outliers start: 38 outliers final: 30 residues processed: 223 average time/residue: 0.2802 time to fit residues: 91.2231 Evaluate side-chains 228 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15209 Z= 0.206 Angle : 0.532 8.440 20719 Z= 0.275 Chirality : 0.039 0.153 2383 Planarity : 0.004 0.038 2616 Dihedral : 9.164 178.075 2164 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.30 % Favored : 93.37 % Rotamer: Outliers : 2.40 % Allowed : 13.11 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1843 helix: 2.08 (0.17), residues: 991 sheet: 1.39 (0.62), residues: 73 loop : -1.41 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1019 HIS 0.006 0.001 HIS B 166 PHE 0.018 0.001 PHE A 793 TYR 0.012 0.001 TYR B 122 ARG 0.003 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: A 1044 LEU cc_start: 0.8800 (tt) cc_final: 0.8468 (mp) REVERT: A 1269 HIS cc_start: 0.7496 (m90) cc_final: 0.7208 (m90) REVERT: A 1379 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4688 (tt) REVERT: B 107 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8695 (pp) outliers start: 39 outliers final: 30 residues processed: 228 average time/residue: 0.2735 time to fit residues: 92.4782 Evaluate side-chains 228 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15209 Z= 0.177 Angle : 0.532 13.919 20719 Z= 0.273 Chirality : 0.038 0.156 2383 Planarity : 0.004 0.036 2616 Dihedral : 9.067 179.299 2164 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.25 % Favored : 93.48 % Rotamer: Outliers : 1.91 % Allowed : 13.85 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1843 helix: 2.18 (0.17), residues: 990 sheet: 1.40 (0.62), residues: 73 loop : -1.37 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1019 HIS 0.007 0.001 HIS A 352 PHE 0.014 0.001 PHE A 411 TYR 0.011 0.001 TYR A 153 ARG 0.004 0.000 ARG A1375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 991 THR cc_start: 0.8696 (m) cc_final: 0.8429 (m) REVERT: A 1044 LEU cc_start: 0.8811 (tt) cc_final: 0.8500 (mp) REVERT: A 1269 HIS cc_start: 0.7472 (m90) cc_final: 0.7194 (m90) REVERT: A 1379 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4761 (tt) REVERT: B 122 TYR cc_start: 0.8422 (m-80) cc_final: 0.8147 (m-80) outliers start: 31 outliers final: 29 residues processed: 223 average time/residue: 0.2835 time to fit residues: 92.4086 Evaluate side-chains 227 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 681 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15209 Z= 0.290 Angle : 0.576 7.756 20719 Z= 0.299 Chirality : 0.041 0.248 2383 Planarity : 0.004 0.040 2616 Dihedral : 9.139 175.999 2164 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.01 % Favored : 92.72 % Rotamer: Outliers : 2.22 % Allowed : 13.78 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1843 helix: 2.03 (0.17), residues: 990 sheet: 1.38 (0.63), residues: 73 loop : -1.45 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.006 0.001 HIS B 166 PHE 0.019 0.002 PHE A 411 TYR 0.015 0.002 TYR A 153 ARG 0.004 0.000 ARG A1375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8392 (tpp) cc_final: 0.7971 (ttm) REVERT: A 800 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7309 (p90) REVERT: A 1269 HIS cc_start: 0.7501 (m90) cc_final: 0.7241 (m90) REVERT: A 1379 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4750 (tt) REVERT: B 147 MET cc_start: 0.7831 (tmm) cc_final: 0.7329 (tmm) outliers start: 36 outliers final: 32 residues processed: 222 average time/residue: 0.2818 time to fit residues: 92.9838 Evaluate side-chains 229 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0040 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS A 681 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111679 restraints weight = 31941.556| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.13 r_work: 0.2885 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15209 Z= 0.146 Angle : 0.519 8.586 20719 Z= 0.270 Chirality : 0.038 0.218 2383 Planarity : 0.004 0.076 2616 Dihedral : 8.983 179.020 2164 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.92 % Favored : 93.80 % Rotamer: Outliers : 1.35 % Allowed : 14.77 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1843 helix: 2.28 (0.18), residues: 983 sheet: 1.32 (0.62), residues: 73 loop : -1.33 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A 352 PHE 0.009 0.001 PHE A 801 TYR 0.016 0.001 TYR A1088 ARG 0.004 0.000 ARG A1375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.89 seconds wall clock time: 61 minutes 43.47 seconds (3703.47 seconds total)